A NGS analysis pipeline.


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Documentation for package ‘HTSeqGenie’ version 4.34.0

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analyzeVariants Calculate and process Variants
annotateVariants Annotate variants via vep
buildGenomicFeaturesFromTxDb Build genomic features from a TxDb object
callVariantsGATK Variant calling via GATK
checkGATKJar Check for the GATK jar file
detectRRNA Detect rRNA Contamination in Reads
excludeVariantsByRegions Filter variants by regions
gatk gatk
generateSingleGeneDERs generateSingleGeneDERs
getRRNAIds Detect reads that look like rRNA
getTabDataFromFile Load tabular data from the NGS pipeline result directory
hashCoverage Hashing function for coverage
hashVariants Hashing function for variants
hashVector Hashing function for vector
HTSeqGenie Package overview
isSparse isSparse
markDuplicates markDuplicates
markDups markDups
realignIndels realignIndels
realignIndelsGATK Realign indels via GATK
runPipeline Run the NGS analysis pipeline
runPipelineConfig Run the NGS analysis pipeline
setupTestFramework setup test framework
TP53GenomicFeatures Demo genomic features around the TP53 gene
vcfStat Compute stats on a VCF file
wrap.callVariants Variant calling
writeVCF writeVCF